yarn
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
Bioconductor version: 3.24 · Package version: 1.39.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("yarn")Details
| Maintainer | Joseph N Paulson <paulson.joseph@gene.com> |
| Author | Joseph N Paulson [aut, cre], Cho-Yi Chen [aut], Camila Lopes-Ramos [aut], Marieke Kuijjer [aut], John Platig [aut], Abhijeet Sonawane [aut], Maud Fagny [aut], Kimberly Glass [aut], John Quackenbush [aut] |
| License | Artistic-2.0 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, Clustering, GeneExpression, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/yarn/ |
Citation
From within R, enter citation("yarn"):
Joseph N Paulson, Cho-Yi Chen, Camila Lopes-Ramos, Marieke Kuijjer, John Platig, Abhijeet Sonawane, Maud Fagny, Kimberly Glass, John Quackenbush. yarn: YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization. doi:10.18129/B9.bioc.yarn, R package version 1.39.0, https://bioconductor.org/packages/yarn.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | yarn_1.39.0.tar.gz |
| Windows binary (x86_64) | yarn_1.39.0.zip |
| macOS binary (arm64) | yarn_1.39.0.tgz |
| macOS binary (x86_64) | yarn_1.39.0.tgz |
Dependencies
Depends: Biobase
Imports: biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro
Suggests: knitr, rmarkdown, testthat (>= 0.8)